I understand, but my point was that the avr/io.h equivalent for ARM doesn't exist and its not going to exist. You'll never find a "sam/pio.h" that works as a drop-in replacement for avr/io.h, because it can't be done.
The call to avr/io.h was shown in the compiler error statement as coming from line 25 in twi.c.
This is strange because the Wire library is one of the first library that was ported to Due, and I saw many reports from users that used it successfully.
Are you using the Wire library found in arduino-1.5.1?